# 1) Amphibia - Brazil ----------------------------------------------------

## Article:
# Segalla, M; Berneck, B.;Canedo, C.; Caramaschi, U.; Cruz, C.A.G.; Garcia, P. C. A.; Grant, T.; Haddad, C. F. B.; Lourenço, A. C.; Mangia, S.; Mott, T.; Nascimento, L. Toledo, L. F.; Werneck, F.; Langone, J. A. (2021). List of Brazilian Amphibians. Herpetologia Brasileira, 10(1), 121–216. https://doi.org/10.5281/zenodo.4716176

## Download file:
# download.file(url = "https://zenodo.org/record/4716176/files/Segalla_et_al_2021_HB.pdf?download=1",
#             destfile = "data/raw/Segalla et al. 2021 - Amphibia.pdf",
#             mode = "wb")

# Wrangling pdf
amp_splist <- pdftools::pdf_text(here::here("data/raw/Segalla et al. 2021 - Amphibia.pdf")) %>%
    readr::read_lines(.) %>%
    dplyr::as_tibble(., .name_repair = "minimal") %>%
    dplyr::mutate(value = stringr::str_replace(value, "225", "225."),
           value = stringr::str_replace(value, "3547", "347."),
           value = stringr::str_replace(value, "6797", "677."),
           value = stringr::str_replace(value, "10343", "1033.")) %>%
    dplyr::filter(stringr::str_detect(value, "^\\s{1,}\\d{1,4}\\.")) %>%
    dplyr::mutate(value = stringr::str_squish(value),
                  value = stringr::str_replace(value, "\\. ", "/")) %>%
    tidyr::separate(col = value,
                    into = c("id_list", "species"),
                    sep = "/") %>%
    dplyr::mutate(species = stringr::str_extract(species, "\\w+\\s\\w+\\-?\\w+")) %>%
    tidyr::separate(col = species,
                    into = c("gender", "epithet"),
                    sep = " ",
                    remove = FALSE)

## Saving csv file
readr::write_csv(amp_splist, here::here("data/processed/amp_splist.csv"))

library(rentrez)

library(rredlist)

datatable(amp_gbif, filter = "top",  
          options = list(searchHighlight = TRUE, 
                       pageLength = 15))